Fix figure output folder in LGEA.Epi

r.scripts/sc_QuSAGE.LGEA.Epi.R

@@ -144,7 +144,7 @@ for (j in 1:3){
   } else if (j==3) {
     pop <- "hCGC"
   }
-  png(paste0("./genesets/",opt$g,"/global",sub.folder,"/correlation/QuSAGE_",pop,".png"),1000,1000,pointsize=20)
+  png(paste0("./analysis/",opt$g,"/global",sub.folder,"/correlation/QuSAGE_",pop,".png"),1000,1000,pointsize=20)
   for (i in Epi){
     qs <- get(paste0("qs.results.",i))
     if (i==Epi[1]){
@@ -177,7 +177,7 @@ sc10x.Group@ident <- plyr::mapvalues(x=sc10x.Group@ident,from=Epi,to=merge.clust
 sc10x.Group <- StashIdent(object=sc10x.Group,save.name="LGEA.Epi")
 
 #generate EpiPop tSNE
-png(paste0("./genesets/",opt$g,"/global",sub.folder,"/tSNE_LGEA.Epi.png"),1000,1000,pointsize=20)
+png(paste0("./analysis/",opt$g,"/global",sub.folder,"/tSNE_LGEA.Epi.png"),1000,1000,pointsize=20)
 plot <- TSNEPlot(object=sc10x.Group,pt.size=5,do.label=TRUE,label.size=10,do.return=TRUE)
 plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20),legend.text=element_text(size=20))
 plot <- plot+guides(colour=guide_legend(override.aes=list(size=10)))
@@ -256,7 +256,7 @@ for (i in 1:Number.Clusters){
         }}}}}
 sc10x.Group@ident <- plyr::mapvalues(x=sc10x.Group@ident,from=1:Number.Clusters,to=merge.cluster)
 sc10x.Group <- StashIdent(object=sc10x.Group,save.name="LGEA.EpiSubPop")
-png(paste0("./genesets/",opt$g,"/global",sub.folder,"/tSNE_LGEA.EpiSubPop.png"),1000,1000,pointsize=20)
+png(paste0("./analysis/",opt$g,"/global",sub.folder,"/tSNE_LGEA.EpiSubPop.png"),1000,1000,pointsize=20)
 plot <- TSNEPlot(object=sc10x.Group,pt.size=5,do.label=TRUE,label.size=10,do.return=TRUE)
 plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20),legend.text=element_text(size=20))
 plot <- plot+guides(colour=guide_legend(override.aes=list(size=10)))